Galaxy |

Seurat NormaliseData tool metadata

Miscellaneous

Name: Seurat NormaliseData

Description: normalise data

Id: seurat_normalise_data

Guid: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/3.2.3+galaxy0

Version: 3.2.3+galaxy0

Version command string: echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0

toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/3.2.3+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/3.1.2+galaxy0

toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/3.1.1+galaxy0

toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/3.1.1_0.0.6+galaxy0

toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/2.3.1+galaxy1

seurat_normalise_data

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

seurat-scripts

0.3.0

package

Additional information about this tool

Command:

seurat-normalise-data.R


    #if $input.format == "anndata"
        --input-object-file input.h5ad --input-format anndata
    #else if $input.format == "loom"
        --input-object-file input.loom --input-format loom
    #else if $input.format == "rds_seurat"
        --input-object-file '$input.rds_seurat_file' --input-format seurat
    #else if $input.format == "rds_sce"
        --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
    #else if $input.format == "h5seurat"
        --input-object-file input.h5seurat --input-format h5seurat
    #end if
   
#if $norm:
    --normalization-method $norm
#end if
#if $assay:
    --assay-type '$assay'
#end if
#if $scale:
    --scale-factor $scale
#end if

    #if $format == "anndata"
        --output-object-file '$anndata_file' --output-format anndata
    #else if $format == "loom"
        --output-object-file seurat_obj.loom --output-format loom
    #else if $format == "rds_seurat"
        --output-object-file '$rds_seurat_file' --output-format seurat
    #else if $format == "rds_sce"
        --output-object-file '$rds_sce_file' --output-format singlecellexperiment
    #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells.rds

name: value

E-MTAB-6077-3k_features_90_cells.rds
value